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Register a new userModeling Discrete Combinatorial Systems as Alphabetic Bipartite Networks: Theory and Applications
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Life and language are discrete combinatorial systems (DCSs) in which the basic building blocks are finite sets of elementary units: nucleotides or codons in a DNA sequence and letters or words in a language. Different combinations of these finite units give rise to potentially infinite numbers of genes or sentences. This type of DCS can be represented as an Alphabetic Bipartite Network ($alpha$-BiN) where there are two kinds of nodes, one type represents the elementary units while the other type represents their combinations. There is an edge between a node corresponding to an elementary unit $u$ and a node corresponding to a particular combination $v$ if $u$ is present in $v$. Naturally, the partition consisting of the nodes representing elementary units is fixed, while the other partition is allowed to grow unboundedly. Here, we extend recently analytical findings for $alpha$-BiNs derived in [Peruani et al., Europhys. Lett. 79, 28001 (2007)] and empirically investigate two real world systems: the codon-gene network and the phoneme-language network. The evolution equations for $alpha$-BiNs under different growth rules are derived, and the corresponding degree distributions computed. It is shown that asymptotically the degree distribution of $alpha$-BiNs can be described as a family of beta distributions. The one-mode projections of the theoretical as well as the real world $alpha$-BiNs are also studied. We propose a comparison of the real world degree distributions and our theoretical predictions as a means for inferring the mechanisms underlying the growth of real world systems.
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We introduce and study random bipartite networks with hidden variables. Nodes in these networks are characterized by hidden variables which control the appearance of links between node pairs. We derive analytic expressions for the degree distribution, degree correlations, the distribution of the number of common neighbors, and the bipartite clustering coefficient in these networks. We also establish the relationship between degrees of nodes in original bipartite networks and in their unipartite projections. We further demonstrate how hidden variable formalism can be applied to analyze topological properties of networks in certain bipartite network models, and verify our analytical results in numerical simulations.
We analyze the connectivity structure of weighted brain networks extracted from spontaneous magnetoencephalographic (MEG) signals of healthy subjects and epileptic patients (suffering from absence seizures) recorded at rest. We find that, for the activities in the 5-14 Hz range, healthy brains exhibit a sparse connectivity, whereas the brain networks of patients display a rich connectivity with clear modular structure. Our results suggest that modularity plays a key role in the functional organization of brain areas during normal and pathological neural activities at rest.
High-order, beyond-pairwise interdependencies are at the core of biological, economic, and social complex systems, and their adequate analysis is paramount to understand, engineer, and control such systems. This paper presents a framework to measure high-order interdependence that disentangles their effect on each individual pattern exhibited by a multivariate system. The approach is centred on the local O-information, a new measure that assesses the balance between synergistic and redundant interdependencies at each pattern. To illustrate the potential of this framework, we present a detailed analysis of music scores from J.S. Bach, which reveals how high-order interdependence is deeply connected with highly non-trivial aspects of the musical discourse. Our results place the local O-information as a promising tool of wide applicability, which opens new perspectives for analysing high-order relationships in the patterns exhibited by complex systems.
Uncovering factors underlying the network formation is a long-standing challenge for data mining and network analysis. In particular, the microscopic organizing principles of directed networks are less understood than those of undirected networks. This article proposes a hypothesis named potential theory, which assumes that every directed link corresponds to a decrease of a unit potential and subgraphs with definable potential values for all nodes are preferred. Combining the potential theory with the clustering and homophily mechanisms, it is deduced that the Bi-fan structure consisting of 4 nodes and 4 directed links is the most favored local structure in directed networks. Our hypothesis receives strongly positive supports from extensive experiments on 15 directed networks drawn from disparate fields, as indicated by the most accurate and robust performance of Bi-fan predictor within the link prediction framework. In summary, our main contribution is twofold: (i) We propose a new mechanism for the local organization of directed networks; (ii) We design the corresponding link prediction algorithm, which can not only testify our hypothesis, but also find out direct applications in missing link prediction and friendship recommendation.
Any physiochemical variable (Ym) is always determined from certain measured variables {Xi}. The uncertainties {ui} of measuring {Xi} are generally a priori ensured as acceptable. However, there is no general method for assessing uncertainty (em) in the desired Ym, i.e. irrespective of whatever might be its system-specific-relationship (SSR) with {Xi}, and/ or be the causes of {ui}. We here therefore study the behaviors of different typical SSRs. The study shows that any SSR is characterized by a set of parameters, which govern em. That is, em is shown to represent a net SSR-driven (purely systematic) change in ui(s); and it cannot vary for whether ui(s) be caused by either or both statistical and systematic reasons. We thus present the general relationship of em with ui(s), and discuss how it can be used to predict a priori the requirements for an evaluated Ym to be representative, and hence to set the guidelines for designing experiments and also really appropriate evaluation models. Say: Y_m= f_m ({X_i}_(i=1)^N), then, although: e_m= g_m ({u_i}_(i=1)^N), N is not a key factor in governing em. However, simply for varying fm, the em is demonstrated to be either equaling a ui, or >ui, or even <ui. Further, the limiting error (d_m^(Lim.)) in determining an Ym is also shown to be decided by fm (SSR). Thus, all SSRs are classified into two groups: (I) the SSRs that can never lead d_m^(Lim.) to be zero; and (II) the SSRs that enable d_m^(Lim.) to be zero. In fact, the theoretical-tool (SSR) is by pros and cons no different from any discrete experimental-means of a study, and has resemblance with chemical reactions as well.
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